Abstract Detail

Systematics Section/ASPT

Wysocki, William P. [1], Clark, Lynn G. [2], Kelchner, Scot A. [3], Burke, Sean V. [1], Pires, J. Chris [4], Edger, Pat [5], Mayfield-Jones, Dustin [6], Triplett, Jimmy K. [7], Columbus, J. Travis [8], Ingram, Amanda L. [9], Duvall, Melvin R. [10].

A Multi-Step Comparison of Short-Read Full Plastome Sequence Assembly Methods in Grasses.

Recent technological advances have allowed full chloroplast genome (plastome) phylogenomic analyses of plants to become economically feasible and so increasingly popular.  Although next generation short read sequencing allows for full plastomes to be sequenced relatively rapidly, it requires additional software and algorithms to assemble these reads into complete plastomes.  Here we compare the use of three de novo assemblers combined with three contig assembly methods for the processing of single-end short reads. Seven plastome sequences were analyzed.  Three of these were Sanger-sequenced.  The other four were assembled from short, single-end read files generated from next generation libraries. These plastomes represented a total of six grass species (Poaceae), one of which was sequenced in duplicate by the two methods to allow direct comparisons for accuracy. Enumeration of missing sequence and ambiguities allowed for assessments of completeness and efficiency. All methods that used de Bruijn-based de novo assemblers were shown to produce assemblies comparable to the Sanger-sequenced plastomes but were not equally efficient.  Contig assembly methods that utilized automatable and repeatable processes were more efficient and advantageous when applied to larger scale studies.  However, contig assembly methods that were less automatable and required more manual attention did show utility in determining plastomes with lower read depths that were not able to be assembled with automatable procedures.  The methods here, which were exclusively used for grass plastomes, can also be applied to the assembly of plastomes from other plant groups.

1 - Northern Illinois University, Biological Sciences, 1425 W. Lincoln Hwy, DeKalb, IL, 60115, USA
2 - Iowa State University, Department Of Ecology, Evolution, And Organismal Biology, 251 Bessey Hall, Ames, IA, 50011-1020, USA
3 - Idaho State University, Department Of Biological Sciences, 921 South 8th Ave., Stop 8007, Pocatello, ID, 83209-8007, USA
4 - University Of Missouri, 371 Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211-7310, USA
5 - University of California, Department of Plant and Microbial Biology, Berkeley, CA, 94794, USA
6 - University of Missouri - Columbia, Division of Biological Sciences
7 - Jacksonville State University, 700 Pelham Road North, Jacksonville, AL, 36265, USA
8 - Rancho Santa Ana Botanic Garden, 1500 North College Avenue, Claremont, CA, 91711-3157, USA
9 - Wabash College, Department Of Biology, P.O. BOX 352, CRAWFORDSVILLE, IN, 47933, USA
10 - NORTHERN ILLINOIS UNIVERSITY, Department Of Biological Sciences, 1425 W Lincoln Hwy, DEKALB, IL, 60115-2861, USA

Keywords:
phylogenomics
next-generation sequencing
plastome
Poaceae.

Presentation Type: Oral Paper:Papers for Sections
Session: 34
Location: Evergreen/Grove
Date: Wednesday, July 30th, 2014
Time: 11:15 AM
Number: 34012
Abstract ID:396
Candidate for Awards:None